Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	V	L	I	N	E	K	L	H	S	R	R	L	K	W	R	W	P	L	S	R	Q	V	T	L	S	I	G	T	L	A	V	L	L	T	V	W	W	T	V	A	T	L	Q	L	I	S	P	L	F	L	P	P	P	Q	Q	V	L	E
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?	?																													?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		K	L	L	T	I	A	G	P	Q	G	F	M	D	A	T	L	W	Q	H	L	A	A	S	L	T	R	I	M	L	A	L	F	A	A	V	L	F	G	I	P	V	G	I	A	M	G	L	S	P	T	V	R	G	I	L	D	P	I	I	E
Secondary structure
SS confidence
Disorder									?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		L	Y	R	P	V	P	P	L	A	Y	L	P	L	M	V	I	W	F	G	I	G	E	T	S	K	I	L	L	I	Y	L	A	I	F	A	P	V	A	M	S	A	L	A	G	V	K	S	V	Q	Q	V	R	I	R	A	A	Q	S	L	G
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		A	S	R	A	Q	V	L	W	F	V	I	L	P	G	A	L	P	E	I	L	T	G	L	R	I	G	L	G	V	G	W	S	T	L	V	A	A	E	L	I	A	A	T	R	G	L	G	F	M	V	Q	S	A	G	E	F	L	A	T	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.
Sequence		V	V	L	A	G	I	A	V	I	A	I	I	A	F	L	L	E	L	G	L	R	A	L	Q	R	R	L	T	P	W	H	G	E	V	Q
Secondary structure
SS confidence
Disorder																															?		?	?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2onk chain C Region: 15 - 263 Aligned: 233 Modelled: 233 Confidence: 100.0% Identity: 20% PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda Phyre2 PDB 2onk chain C domain 1 Region: 15 - 263 Aligned: 233 Modelled: 233 Confidence: 100.0% Identity: 20% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3fh6 chain F Region: 12 - 266 Aligned: 255 Modelled: 255 Confidence: 100.0% Identity: 13% PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli Phyre2 PDB 3d31 chain D Region: 24 - 261 Aligned: 229 Modelled: 238 Confidence: 100.0% Identity: 19% PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans Phyre2 PDB 3d31 chain C domain 1 Region: 24 - 261 Aligned: 229 Modelled: 238 Confidence: 100.0% Identity: 19% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain F Region: 61 - 259 Aligned: 199 Modelled: 199 Confidence: 100.0% Identity: 14% PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter Phyre2 PDB 2r6g chain F domain 2 Region: 64 - 259 Aligned: 196 Modelled: 196 Confidence: 100.0% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 2r6g chain G domain 1 Region: 13 - 262 Aligned: 248 Modelled: 250 Confidence: 100.0% Identity: 14% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 3dhw chain A domain 1 Region: 76 - 261 Aligned: 186 Modelled: 186 Confidence: 100.0% Identity: 18% Fold: MetI-like Superfamily: MetI-like Family: MetI-like Phyre2 PDB 1umq chain A Region: 160 - 190 Aligned: 31 Modelled: 31 Confidence: 17.4% Identity: 10% PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity Phyre2 PDB 1umq chain A Region: 160 - 190 Aligned: 31 Modelled: 31 Confidence: 17.4% Identity: 10% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1ntc chain A Region: 158 - 190 Aligned: 33 Modelled: 33 Confidence: 13.1% Identity: 18% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1fip chain A Region: 160 - 190 Aligned: 31 Modelled: 31 Confidence: 10.8% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 1eto chain B Region: 160 - 190 Aligned: 31 Modelled: 31 Confidence: 8.9% Identity: 16% Fold: DNA/RNA-binding 3-helical bundle Superfamily: Homeodomain-like Family: FIS-like Phyre2 PDB 3e7l chain D Region: 160 - 190 Aligned: 31 Modelled: 31 Confidence: 8.0% Identity: 10% PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain Phyre2 1 c2onkC_ 2 d2onkc1 3 c3fh6F_ 4 c3d31D_ 5 d3d31c1 6 c2r6gF_ 7 d2r6gf2 8 d2r6gg1 9 d3dhwa1 10 c1umqA_ 11 d1umqa_ 12 d1ntca_ 13 d1fipa_ 14 d1etob_ 15 c3e7lD_

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2onkC_ 100.0 20 PDB header:membrane protein Chain: C: PDB Molecule:molybdate/tungstate abc transporter, permease PDBTitle: abc transporter modbc in complex with its binding protein2 moda 2 d2onkc1 100.0 20 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 3 c3fh6F_ 100.0 13 PDB header:transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: crystal structure of the resting state maltose transporter from e.2 coli 4 c3d31D_ 100.0 19 PDB header:transport protein Chain: D: PDB Molecule:sulfate/molybdate abc transporter, permease PDBTitle: modbc from methanosarcina acetivorans 5 d3d31c1 100.0 19 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 6 c2r6gF_ 100.0 14 PDB header:hydrolase/transport protein Chain: F: PDB Molecule:maltose transport system permease protein malf; PDBTitle: the crystal structure of the e. coli maltose transporter 7 d2r6gf2 100.0 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 8 d2r6gg1 100.0 14 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 9 d3dhwa1 100.0 18 Fold:MetI-like Superfamily:MetI-like Family:MetI-like 10 c1umqA_ 17.4 10 PDB header:dna-binding protein Chain: A: PDB Molecule:photosynthetic apparatus regulatory protein; PDBTitle: solution structure and dna binding of the effector domain2 from the global regulator prra(rega) from r. sphaeroides:3 insights into dna binding specificity 11 d1umqa_ 17.4 10 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 12 d1ntca_ 13.1 18 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 13 d1fipa_ 10.8 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 14 d1etob_ 8.9 16 Fold:DNA/RNA-binding 3-helical bundle Superfamily:Homeodomain-like Family:FIS-like 15 c3e7lD_ 8.0 10 PDB header:transcription regulator Chain: D: PDB Molecule:transcriptional regulator (ntrc family); PDBTitle: crystal structure of sigma54 activator ntrc4's dna binding2 domain

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0